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Microbial Ecology

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Published in: EVS
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Environmental microbiology

M C / Visakhapatnam

8 years of teaching experience

Qualification: M.Sc

Teaches: Biology, Chemistry

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  1. Microbial Ecology Chapter 30
  2. Principles of Microbial Ecology Ecology is study of relationships of organisms to each other and environment Organisms in given area are termed a community — Communities interact with each other and non-living environment This interaction forms an ecosystem
  3. Principles of Microbial Ecology Major ecosystems include — Oceans, rivers, lakes, deserts, marshes, grasslands, forests and tundra Each ecosystem contains certain organisms and characteristic physical conditions Region of earth inhabited by living organisms termed biosphere Ecosystems vary within biosphere in biodiversity and biomass — Biodiversity = number of species present and evenness of distribution — Biomass = weight of all organisms present
  4. Principles of Microbial Ecology Microorganisms play major role in most ecosystems — Role an organism plays in ecosystem is termed ecological niche — Environment immediately surrounding microorganism is termed microenvironment Most relevant to that cell — Often difficult to identify and measure — Macro environment may be more easily measured and is very different from microenvironment
  5. Principles of Microbial Ecology Copynght MeGtaw-HiII C«nparues. Ire. Permassøn 'Of reproduebon or display. Nutrient acquisition — Organisms are categorized according to trophic level Trophic = source of food — Level is intimately related to cyclin! of nutrients — Three general trophic levels Primary producers Consumers Decomposers H2S. NH3 and other reduced energy Radiant energy Pnttury producers Organic (CH20) 1 matter organic matter Sman molecules (including C02) coz
  6. Principles of Microbial Primary producers — Primary producers are autotrophs — Convert carbon dioxide to organic materials — Include Photoautotrophs — Plants — Algae — Cyanobacteria — Anoxygenic phototrophs — All use sunlight for energy Chemoautotrophs — Oxidize inorganic compounds for energy — Primary producers serve as food source for consumers and decomposers Ecology Radiant energy Primary producers
  7. Principles of Microbial Ecology Consumers — Consumers are heterotrophs — Rely on activities of primary producers — Herbivores eat primary producers Termed primary consumers — Carnivores consume herbivores Termed secondary consumers — Carnivores that eat other carnivores Termed tertiary consumers — Chain of consumption called food chain — Interaction between food chains called food webs Organic (CH20) Consumers
  8. Principles of Microbial Ecology Decomposers — Decomposers are heterotrophs that digest remains of primary producers and consumers Partially decomposed organic matter of other trophic levels termed detritus — Decomposers specialize in digestion of complex material Convert them into small molecules — Molecules more readily usable by other organisms — Complete breakdown of organic molecules to inorganic molecules is termed mineralization Decomposers oo
  9. Principles of Microbial Ecology Bacteria in low-nutrient environments — These environments common in nature — Growth in these areas most often in form of biofilm Not restricted to specific environments like lakes and streams — Organisms can also grow in distilled environments of hospital water reservoirs — Microbes can extract amounts of nutrient absorbed by water Growth usually goes unnoticed — Can have serious consequences in hospitalized patients — Organisms that survive in low nutrient environments often have highly efficient transport systems for nutrient procurement
  10. Principles of Microbial Ecology Microbial competition and antagonism — Results of competition evident among organisms Ability to compete is generally related to rate of growth — Organisms that multiply faster yield larger population and use more nutrient supply — Antagonism helps determine make-up of population Bacteriocines produced by certain species to kill other strains — Form of chemical antagonisms Copyright O The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Growth Transfers and more growth Coccus Rod
  11. Principles of Microbial Ecology Microorganisms and environmental change — Environmental change often results in alterations in a bacterial community In order for organism to survive in new conditions it must adapt to altered environment — In response to new stimuli microbes stop producing enzymes that serve no purpose Mutants within a population may remain in minority in current population — Mutation may make organism well suited for new changed environment
  12. Principles of Microbial Ecology Microbial communities — Microorganisms often grow in communities attached to some solid surface or at air-water interface Usually grow in biofilms or microbial mats
  13. Principles of Microbial Ecology — Microbial mat is thick, dense organized structure composed of distinct layers — Frequently green, pink and black Green layer is uppermost — Typically composed of various species of cyanobacteria Pink layer directly below green — Consists of purple sulfur bacteria Black layer is at bottom — Formed by iron molecules reacting with hydrogen sulfide Hydrogen sulfide produced by bacteria called sulfate reducers Copyright O The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
  14. Principles of Microbial Ecology Studying microbial ecology — Microscopic methods used to allow examination of composition of microbial populations — Fluorescent in situ hybridization (FISH) uses nucleic acid probes to cells containing specific nucleotide sequences — Confocal scanning electron microscopes allow screening of sectional views of 3D specimens
  15. Principles of Microbial Ecology Studying microbial ecology — Polymerase chain reaction (PCR) can be used to detect certain organisms and assessment of population characteristics — Denaturing gradient gel electrophoresis (DGGE) is used to separate and examine a set of amplified sequences within a genome — Genomics is particularly useful in study of microbial ecology Sequence information gained from one organism can be applied to others
  16. Aquatic Habitats Deep lakes and oceans have characteristic zones — Zones influence distribution of microbial populations Upper zone has sufficient light penetration to support photosynthetic microorganisms — Organic material produced by these organisms descends and is metabolized by heterotrophs Copyright O The McGraw-Hill Corrvanies. Inc. Permission required lot reproduction or display.
  17. Aquatic Habitats In oligotrophic waters growth of photosynthetic organisms is limited due to lack of certain nutrients Eutrophic waters support robust multiplication of photosynthetic organisms due to rich content of nutrient — Activity of surface organisms produce nutrient compounds for heterotrophic growth in lower levels — Heterotrophs consume oxygen during metabolism of nutrient Waters may become hypoxic — Leads to death of resident aquatic wildlife
  18. Aquatic Habitats Marine environments — Range from deep sea to shallower coastal regions Nutrients scarce in deep sea regions Nutrients abundant in shallow coastal region — Seawater contains high salt concentration Supports halophilic organisms — Ocean waters usually oligotrophic Limits growth of microorganisms — Ecology of inshore areas not as stable as deep sea Can be dramatically affected by nutrient-rich runoff — Consequence = populations of algae and cyanobacteria flourish » Oxygen is consumed and regions become hypoxic Hypoxic regions termed "dead zone"
  19. Aquatic Habitats Freshwater environments — Lakes and streams most obvious freshwater environments Type and numbers of organisms inhabiting freshwater depend on multiple factors — Light — Concentration of dissolved oxygen — Nutrients — Temperature
  20. Aquatic Habitats Freshwater environments — Oligotrophic lakes in temperate climates have anaerobic layers due to thermal stratification As a result of seasonal temperature changes Layers include — Epilimnion — Hypolimnion — Thermocline
  21. Aquatic Habitats Freshwater environments — Epilimnion Top layer Generally oxygen rich — Hypolimnion Lower layer May be anaerobic — Thermocline Middle layer Zone of rapid temperature change — Particularly during seasonal changes — As weather cools layers mix Provides oxygen and nutrient to lower levels Epilimnion 250—220C Thermocline 200—1 OOC Hypolimnion 50—40C (a) Seasonal Upwelling (Fall and Spring) Nutrients (b)
  22. Aquatic Habitats Specialized aquatic environments — These include salt lakes Water in these lakes evaporates leaving concentrations of salt much higher than seawater — Extreme halophiles thrive in this environment — Other specialized habitats include iron springs Contains large quantities of ferrous ions Habitats for Gal/ione//a and Sphaeroti/us species — Sulfur springs Support growth of both photosynthetic and non-photosynthetic sulfur bacteria
  23. Terrestrial Habitats Human interest in microbiology of the soil stems from ability of microbes to synthesize a variety of useful chemicals — 500 different antibiotic substances produced by Streptomyces species 50 have useful application in medicine, agriculture and industry — Soil microbes being tested for their ability to degrade toxic chemicals
  24. Terrestrial Habitats Characteristics of soil —Soil is composed of pulverized rock, decaying organic material, air and water Teems with microbial life including bacteria, fungi, algae, protozoa Other life includes insects, worms and plant roots —Soil environment can fluctuate abruptly and dramatically
  25. Terrestrial Characteristics of soil — Soil has multiple layers a.k.a horizons Habitats — Each horizon has distinct characteristics — Topsoil is known as A horizon Dark nutrient-rich uppermost layer Supports plant growth Depth may vary — Subsoil known as B horizon Accumulation of clay, salts and nutrients leached from topsoil C horizon Partially weathered bedrock — Bedrock or R horizon Lowest layer and is unweathered
  26. Terrestrial Habitats Microorganisms of the soil — Density and composition of microbial flora of soil affected by environmental conditions Wet soils unfavorable for growth due to lack of air During drought water availability drops and organisms decrease — Many organisms produce survival forms such as endospores and cysts — Other environmental influences include acidity, temperature and nutrient supply
  27. Terrestrial Habitats Microorganisms of soil — Prokaryotes are most numerous soil inhabitants Physiologic diversity allows colonization of all types of soil — Gram (+) more abundant than Gram (-) » Most common Gram (+) are Bacillus species » Produce endospores that allow survival in soil Fungi are usually found in the top portions of soil due to aerobic nature — Fungi are crucial in decomposing plant matter Some fungi are free living in soil — Others develop symbiotic relationships with certain plant roots
  28. Terrestrial Habitats The rhizosphere — Zone of the soil that adheres to plant roots — Enriched soil fosters growth of microorganisms Concentration of microbes in rhizosphere is generally much higher than in surrounding soil
  29. Biogeochemical Cycling and Energy Flow Biochemical cycles are cyclical paths that elements take as they flow through living and nonliving components of the ecosystem — Living = biotic — Non-living = abiotic Cycles are important — Allows ecosystem to sustain characteristic life forms through recycling of elements Carbon and nitrogen cycle important in the recycling of environmental components
  30. Biogeochemical Cycling and Energy Flow Elements cycle through the ecosystem — Energy does not Energy must be continually added Elements have specific role in metabolism of an organism — They serve three general purposes Biomass production — Element is incorporated into cell material Energy source — Reduced form of the element is used to generate energy Terminal electron acceptor — Electrons from energy source are transferred to oxidized form of element during respiration
  31. Biogeochemical Cycling and Energy Flow Carbon cycle — All organisms are composed of organic molecules — Consumers eat producers to acquire organic carbon for biomass and energy — Decomposers use remains of producers and consumers for same purpose — C02 is produced through the degradation of organic matter — C02 is converted back to organic matter by producers to complete cycle Copyright O The McGraw-Hill Companies, inc. Permission required for reproduction or display. (CH20)n Organic compounds Respiration plants • Animals • Microbes Methane-oxidizing bacteria Methane CH4 Reduced carbon Methanogens Anaerobic microbes Combustion . Wood • Coal • Oil . Gas • peat C02 Oxidized carbon C02 (CH20)n Organic compounds Photosynthesis • Plants • Algae • Cyanobacteria Anaerobic respiration Fermentation Aerobic Anaerobic
  32. Biogeochemical Cycling and Energy Flow Fundamental aspect of the carbon cycle is carbon fixation — Defining characteristic of primary producers They convert C02 to organic carbon — Organic carbon travels through the food chain as primary producers are eaten by primary consumers Primary consumers are eaten by secondary consumers — One form of biomass is transformed into another — Not all organic matter consumed is used to create biomass » Some is used as energy
  33. Biogeochemical Cycling and Energy Flow Rapidly multiplying bacteria play dominate role in the decomposition of animal flesh Certain fungi are responsible for the breakdown of other products such as wood Aerobic conditions are required for degradation — End products are carbon dioxide and water In low oxygen levels decomposition is incomplete — Some carbon dioxide combines with oxygen to produce methane and water as end products
  34. Biogeochemical Cycling and Energy Flow Copyright O The McGraw-Hill Companies, Inc. Permission required for reproduction or displayt Nitrogen cycle — Consumers ingest plants and animals to fulfill both their carbon, energy and nitrogen needs Nitrogen is used solely to build biomass — Prokaryotes are more diverse in their use of nitrogen compounds Some use nitrite and nitrate as terminal electron acceptors Others use ammonium as an energy source Animals eat plants Organic N (plants, micro- organisms) I Plants take Organic N (animals) Nitrogen fixation (symbiotic and free-living) Decomposition Ammonification up nitrogen Lightning 14 N2 Chemical fixatio Denitrification NOE (anaerobic bacteria) Nitrification (Nitrobacter, Nitrospira) NH3 + 1-420 NH4+ + OH-- N itrification (Nitrosomonas) NOE
  35. Biogeochemical Cycling and Energy Flow Nitrogen fixation — Process in which nitrogen gas is reduced to form ammonia Ammonia can be incorporated into cellular material — Animals rely on prokaryotes to convert nitrogen gas to a form that can be assimilated to create biomass — Nitrogenase mediates nitrogen fixation Enzyme complex is readily activated by oxygen Nitrogen fixing microbes called diazotrophs must have mechanism to protect ntirogenase complex from oxygen exposure
  36. Biogeochemical Cycling and Energy Flow May be free living or from symbiotic associations with higher organisms particularly plants Heterocysts are formed by numerous free living diazotrophs to protect nitrogenase from oxygen exposure Others consume oxygen so readily that anaerobic conditions are soon reached
  37. Biogeochemical Cycling and Energy Flow Ammonification — Decomposition process that converts organic nitrogen into ammonia — Wide variety of organisms can degrade proteins Proteins among most prevalent nitrogen-containing organic compounds Organisms break down proteins using extracellular photolytic enzymes that create short peptides or amino acids — Amino groups are removed and ammonia release upon entry into the cell » Ammonia is then used to create biomass
  38. Biogeochemical Cycling and Energy Flow Nitrification — Process that oxidizes ammonium to nitrate Bacteria called nitrifiers do this in a two step process — Ammonia is oxidized to nitrite via the action of genus Nitrosomonas — Nitrite is oxidized to nitrate via actions of genus Nitrobacter — Nitrifiers are obligate aerobes using oxygen as terminal electron acceptor
  39. Biogeochemical Cycling and Energy Flow Nitrification has important consequences in agricultural practices and pollution Nitrification converts ammonium to nitrate which is used by plants — Nitrates in soil rapidly leached from soil by rainwater — Oxidation of ammonia to nitrite can also pose threat in that in sufficient concentration nitrite is toxic Nitrites can be found in ground water and consumed — Nitrite reduces oxygen carrying ability of hemoglobin
  40. Biogeochemical Cycling and Energy Flow Denitrification — Process that converts nitrate to gaseous nitrogen such as nitrous oxide and molecular nitrogen Represents oxidized nitrogen — Pseudomonas species responsible for significant denitirfication — Denitirification is main source of release of nitrogen gases in the atmosphere Contributes to global warming — Process may be used in wastewater treatment as a way to remove nitrate from water More desirable use of process
  41. Biogeochemical Cycling and Energy Flow Copyright O The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Sulfur cycle — Sulfur occurs in living matter in the form of certain amino acids and coenzymes — Key steps in sulfur cycle depend on prokaryotes Use reduced forms of sulfur as energy sources — Hydrogen sulfide and elemental sulfur in particular Others use oxidized forms as terminal electron acceptors — Sulfate Animals eat plants Organic S (plants, micro- Organic S (animals) organisms) Sulfate incorporated into plants SO 42— S oxidation Sulfate reduction (bacteria) (photosynthetic and non-photosynthetic sulfur bacteria) Decomposition (microorganisms) H2S HS oxidation (photosynthetic and non-photosynthetic sulfur bacteria)
  42. Biogeochemical Cycling and Energy Flow Sulfur oxidation — Hydrogen sulfide and elemental sulfur can both serve as energy sources for certain chemolithotrophs — Some bacteria oxidize these molecules to sulfate — Hydrogen sulfide and elemental sulfur are oxidized anaerobically by photosynthetic blue and purple sulfur bacteria Use sunlight as energy but need reduced molecules as source of electrons and reducing power
  43. Biogeochemical Cycling and Energy Flow Sulfur reduction — Under anaerobic conditions sulfate can be used as terminal electron acceptor — Sulfur and sulfur-reducing bacteria and archaea use sulfate in anaerobic respiration Reducing sulfate to hydrogen sulfide
  44. Biogeochemical Cycling and Energy Flow Phosphorus cycle and other cycles — Phosphorus is component of several biological compounds — Most plants and microorganisms readily take up phosphorus as orthophosphate Assimilate it into biomass — In many aquatic habitats growth of primary producers often limited by low concentrations of phosphorus — Other elements such as iron, calcium, zinc, magnesium, cobalt and mercury are also cycled by microorganisms
  45. Biogeochemical Cycling and Energy Flow Symbiotic nitrogen-fixers and plants — Significant relationship in plant growth and crop production Important in both terrestrial and aquatic habitats — Organisms collectively called rhizobia Most agriculturally important nitrogen fixers Tend to be associated with leguminous plants — Association between plants and rhizobia involves chemical communication between partners
  46. Biogeochemical Cycling and Energy Flow O the McGraw-Hu Canpar•i«. Ine- Permis•on rquit.d reproduction or di41av Appropriate bacterial species colonize root cells Substances from root cells cause bacteria to produce nod factors — Induce root hairs to curl Bacteria invade root hair — Move into root cell by infection thread Bacteria cell for bacterioid inside cell — Division of root cell and bacterioids produce root nodules Rhizobium cells attach specifically to cells 0' root hair and enter the cells. The Rhizobium invade Other cells through an infection thread synthesized by the root hair. Rhizobium cells develop into bacteroids, which pack the enlarged plant cells. Nodule Consists Of enlarged plant cells packed with bacteroids. Bacterioids fix nitrogen and release ammonia that diffuses into root cells — Ammonia is assimilated into amino acids for use by plant Bacteria gain nutrients from plant

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